The design and maintenance of navigation channel and water facilities of an harbor which is located at the mouth of river or at the estuary area are difficult due to the complexity of estuarial water and sediment circulation. Effects of deepening navigable waterways, of changing coastline configurations, or of discharging dredged material to the open sea are necessary to be investigated and predicted in terms of water quality and possible physical changes to the coastal environment. A borad analysis of the transport mechanism in the estuary area was made in terms of sediment property, falling velocity, concentration and flow characteristics. In order to simulate the transport processes, a two-dimensional finite element model is developed, which includes erosion, transport and deposition mechanism of suspended sediments. Galerkin’s weighted residual method is used to solve the transient convection-diffusion equation. The fluid domain is subdivided into a series of triangular elements in which a quadratic approximation is made for suspended sediment concentration. Model could deal with a continuous aggregation by stipulating the settling velocity of the flocs in each element. The model provides suspended sediment concentration, bed shear stress, erosion versus deposition rate and bed profile at the given time step.